What is GENESIS?
- “GENeralized-Ensemble SImulation System” mainly developed by the Sugita groups in RIKEN, Japan. (Computational Biophysics Research Team (R-CCS), Theoretical Molecular Science Laboratory (CPR), and Laboratory for biomolecular function simulation (BDR))
- Molecular dynamics and modeling software for bimolecular systems such as proteins, lipids, nucleic acids, glycans, and their complexes.
- Open source software distributed under the LGPLv3 (Version 1.4 or earlier is distributed under the GPLv2.)
Functions of GENESIS
The GENESIS program package is composed of two MD programs (ATDYN, SPDYN) and trajectory analysis tools.
- CHARMM force field, AMBER force field, MARTINI model, Go models (Cα Go, all-atom Go, KB Go, and AICG2+), and DNA/RNA models
- Energy minimization and molecular dynamics simulations
- Leapfrog, velocity Verlet, and RESPA integrators
- SHAKE/RATTLE, SETTLE, and LINCS algorithms for bond constraint
- Bussi, Langevin, and Berendsen thermostat/barostat in the NVT, NPT, NPAT, and NPγT ensembles
- Replica-exchange molecular dynamics method (REMD) in temperature, pressure, and surface-tension space
- Generalized replica-exchange with solute tempering (gREST)
- Replica-exchange umbrella sampling (REUS) with collective variables
- Multi-dimensional REMD method (T-REMD/P-REMD, T-REMD/REUS, gREST/REUS, etc)
- Gaussian accelerated molecular dynamics method (GaMD, GaREUS)
- String method for reaction pathway search
- Hybrid QM/MM (quantum mechanics/molecular mechanics) calculation
- Implicit solvent model (Generalized Born/Solvent Accessible Surface Area model)
- Cryo-EM flexible fitting using all-atom, CG, and implicit solvent models with MD, REMD, and REUS
- Free-energy perturbation method (FEP)
- Anharmonic vibrational analysis using SINDO
- Steered MD and Targeted MD simulations
- Restrained MD simulations (Distance, angle, dihedral angle, position, etc)
- Hybrid MPI+OpenMP, hybrid CPU+GPGPU, mixed double+single precision calculations
- Highly-parallelized Particle mesh Ewald method (PME)
- Scalable MD simulations for huge systems (> 100,000,000 atoms)
- Trajectory analysis tools (RMSD, RMSF, PCA, WHAM, MBAR, etc.)
- Spatial decomposition analysis (SPANA)
How to cite GENESIS
Any published work which uses GENESIS 1.0 or before might include the reference:
J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita, WIREs Comput. Mol. Sci., 5, 310-323 (2015).
Any published work which uses GENESIS 1.1.x or 1.2.x should cite the following reference:
C. Kobayashi, J. Jung, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, M. Kamiya, and Y. Sugita, J. Compute. Chem. 38, 2193-2206 (2017) (DOI: 10.1002/jcc.24874).